I do not know that whoever considered ViTharv intercourse as rape has even watched the sequence or not. Firstly a rapist does not hesitate or feel guilty and helpless to touch the woman, Atharva clearly was helpless, he had tears in his eyes before he initiated because he knew that Vividha was dying and he had to do it to save her.
Now post that incident, when Vividha woke up, she saw herself under the blanket, naked and Atharva throwing back her clothes, she blushes and she has no feeling of disgust and pain in her gestures, a woman who enjoys sex and has pleasure usually end up behaving like this, and a woman who has been taken advantage of will be dizzy and traumatized the entire time as she would try to connect the dots and even question the man that how dare he did that.
Infact Atharva was more upset about it than that of Vividha as he knew that whatever had happened was uncalled for, he was not prepared for penetrating her of course, neither he was dying to do her, had this been the case then he had enough chances and privileges given Vividha would be ready by his one call, knowing how madly they loved each other.
Leaves, it is baffling that some body as rational like you has ended up with this theory that Atharva has raped her, he has always been a man who respected woman, his mother has gone through a life where she was tagged as a mistress, he is the victim of his parents deed, he suffered due to a lack of father's name, and he would be the last person to take advantage and use vividha, the same vividha whom he has loved and wanted so dearly, the same woman whom he worshiped like a goddess.